The Saints objected to the language Clattenburg used in an exchange with the England midfielder during last month's 2-1 defeat at Everton.
This complaint was dismissed by the Professional Game Match Officials Limited (PGMOL), but the club were unhappy with the verdict and called for Clattenburg not to officiate games involving Southampton until the 'matter is resolved.'
The FA now appear to have put an end to the dispute by ruling that the match official will not face any action.
A statement from the FA said: "The FA can confirm it received a complaint from Southampton concerning referee Mark Clattenburg and his alleged comments made to their player Adam Lallana.
"The FA has given its full consideration to this matter and it is our view that the comments, as disclosed in Southampton's letter of complaint, do not constitute misconduct under the FA's rules.
"Consequently, the FA will not be taking any further action in relation to this matter and now considers this case to be closed."
The exchange in question is believed to have occurred after Clattenburg had turned down vociferous Southampton appeals for a penalty.
The letter from Southampton claimed Clattenburg said to Lallana: "You are very different now, since you've played for England. You never used to be like this."